Biology subjects

Bai, H.

Publications and source records attributed to Bai, H..

At least 19 recordsLinked to original sources

bioRxiv2026

Co-targeting KRAS and BCL-2 induces pyroptosis and antitumor tertiary lymphoid structures

Mutant KRAS drives lung tumorigenesis through both cell-intrinsic and cell-extrinsic mechanisms, yet mutation subtype-specific differences in metabolic regulation and immune evasion remain incompletely understood. Here we show that the KRAS G12D mutation, particularly in the KRAS/STK11 co-mutant (KL) context, is associated with poor prognosis and a suppressed immune microenvironment characterized by impaired antigen presentation. At the cell-intrinsic level, G12D exhibits weakened interaction with hexokinase 1 (HK1), reduced spare respiratory capacity, and diminished mitochondrial stress resistance compared with G12C. Based on this mitochondrial vulnerability, we screened a panel of clinically available agents that induce mitochondrial stress and identified that co-targeting KRAS and BCL-2 synergistically triggers GSDME-mediated pyroptosis predominantly in G12D tumors. This combination further induces functional tertiary lymphoid structures (TLS) in vivo. Immune cell depletion experiments further demonstrate that the antitumor efficacy is dramatically dependent on B cells. Moreover, this treatment strategy induced membrane attack complex (MAC) deposition in situ and elicited memory antitumor responses. Collectively, these findings establish that combined KRAS and BCL-2 inhibition elicits pyroptosis and TLS formation, leading to B-cell-dependent in situ and memory antitumor immunity, providing a mechanistic rationale for targeting mitochondrial-immune crosstalk in KRAS G12D-mutant lung cancer.

cancer biology↗

bioRxiv2026

Impaired Peroxisome Import Drives Cellular Senescence through SCAF1-Dependent Suppression of Mitoribosome Biogenesis

Communication between peroxisomes and mitochondria is essential for cellular metabolic homeostasis, yet how peroxisomal import stress impacts mitochondria function during aging and cellular senescence remains poorly defined. Using a genome-wide CRISPR screening in HEK293 cells under peroxisome import stress, we identified SCAF1 (SR-related CTD-associated factor 1) a known canonical nuclear pre-mRNA splicing factor, as an essential regulator of mitochondrial homeostasis. Under peroxisome stress SCAF1 undergoes proteolytic processing and translocates to the mitochondria, where its N-terminal region acts as an autonomous repressor module that blocks mitoribosomal subunit joining. Consequently, SCAF1 depletion accelerates subunit joining and elevates oxidative phosphorylation protein levels, whereas its overexpression in IMR90 fibroblast cells triggers robust cellular senescence characterized by increased senescence associated {beta} gal staining. Together, our findings uncover a stress-responsive peroxisome-to-mitochondria signaling axis mediated by SCAF1 translocation. This pathway directly modulates mitoribosome assembly to maintain translational homeostasis, providing a precise molecular mechanism for how upstream peroxisomal decline drives downstream mitochondrial dysfunction and cellular senescence.

cell biology↗

bioRxiv2026

Spatial transcriptomics reveals selective vulnerability of cardiac neural crest-derived glial cells in human myocardial infarction

Cardiac neural crest-derived glial cells (CNGs) are recently identified glial cells that support cardiac autonomic innervation and maintain sympathetic-parasympathetic balance. Their fate in myocardial infarction (MI) is unknown. Here, we analyzed 16 human cardiac spatial transcriptomes spanning normal myocardium (n=4), infarct zone (n=5), border zone (inner, n=1; outer, n=3), and remote zone (n=3). CNGs (S100B+/GFAP+, CD68- spots) were selectively lost along a spatial gradient from healthy tissue to the infarct core (Spearman rho = -0.92, p = 4.5 x 10-7). Tissue-area-corrected analysis confirmed that CNG loss (26% retained in infarct zone vs. normal; p = 0.016) vastly exceeded overall tissue loss, indicating selective vulnerability rather than bulk tissue destruction. Mechanistically, oxidative phosphorylation (OXPHOS) activity in CNG-positive spots correlated positively with CNG survival (partial rho = 0.65, p = 0.009 after controlling for spot composition), consistent with a high metabolic demand underlying their ischemic sensitivity. Pyroptosis - but not ferroptosis or apoptosis - signatures correlated with CNG loss (partial rho = -0.67, p = 0.006). These findings identify CNGs as selectively vulnerable cellular components of the cardiac autonomic system in MI and nominate metabolic failure and pyroptosis as candidate mechanisms, providing a spatially resolved foundation for future mechanistic and interventional studies.

bioinformatics↗

bioRxiv2026

Age-Associated Behavioral Alterations in Laboratory-Housed Octodon degus

Octodon degus are long-lived, diurnal, and highly social rodents increasingly used in studies of aging and neurodegeneration. However, behavioral profiles of aged laboratory-housed degus remain incompletely characterized, limiting the interpretation of aging-associated functional and molecular phenotypes in this species. Here, we evaluated age-associated changes in locomotor activity, open-field exploration, social novelty behavior, and manually scored ethological responses in young and old degus maintained under long-term laboratory housing conditions. Automated behavioral tracking was performed during open-field testing and three-chamber social behavior testing. During open-field testing, old degus showed increased locomotor activity compared with young animals, including greater total distance moved, higher mean velocity, increased moving frequency, and longer cumulative movement duration. Old degus also showed increased center-zone duration and reduced thigmotaxis score. Manual ethological scoring revealed increased rearing and fecal boli in old animals during open-field exposure. In the three-chamber social behavior assay, young degus showed higher investigation frequency toward the novel intruder than toward the familiar cagemate, whereas old degus showed a lower social novelty discrimination index compared with young animals. Sex-stratified analyses did not identify significant male-female differences within young or old groups for the major open-field or social novelty metrics examined. Together, these findings indicate that aging in laboratory-housed degus is associated with a mixed behavioral profile involving increased stress-related ethological responses and reduced social novelty preference reminiscent of dementia-like behavioral changes observed in Alzheimers disease. This behavioral framework provides a practical reference for future studies examining behavioral heterogeneity and molecular correlates of brain aging in degus. Lay SummaryOctodon degus are long-lived, highly social rodents that are increasingly used to study aging and age-related neurodegenerative disorders. However, interpreting behavioral changes in aged degus requires a clear understanding of how aging affects activity, exploration, social behavior, and stress-related responses under laboratory housing conditions. In this study, we compared young and old degus using open-field testing, three-chamber social behavior testing, automated video tracking, and manual scoring of selected behaviors. Aged degus did not show a simple reduction in behavioral activity. Instead, they showed increased movement during behavioral testing, increased rearing behavior, greater exploration of the center of the open-field arena, and increased fecal output during open-field exposure. These findings suggest that aged degus show increased exploratory activity together with altered stress-related responses in a novel environment. Aged degus also showed reduced preference for investigating a novel social partner, consistent with a dementia-like cognitive impairment. Together, these results define a behavioral profile of aged laboratory-housed degus and provide a practical reference for future studies using this species to investigate aging, social behavior, and neurodegeneration-related phenotypes.

neuroscience↗

bioRxiv2026

Symptomatic human norovirus infection in zebrafish embryos uncovers neural infection and extracellular vesicle-mediated transmission dynamics

Human norovirus (hNoV) is the leading global cause of acute gastroenteritis, imposing a substantial health and economic burden worldwide. Progress in understanding hNoV pathogenesis has been hindered by the lack of tractable small-animal models that recapitulate symptomatic infection. Although zebrafish larvae support hNoV replication, infection remains asymptomatic, limiting their utility for studying disease mechanisms and host-pathogen interactions. In this study, we report that the zebrafish embryo infection model, in which microinjection of hNoV at the early cell stage, resulted in robust systemic viral replication accompanied by overt pathological manifestations, including pericardial and renal edema, yolk and cranial opacity, and mortality by 3 days post-infection. Disease severity displayed marked individual variability and correlated closely with viral burden. Integrated multi-omics analyses, including bulk transcriptomics, untargeted metabolomics, and single-cell RNA sequencing, demonstrated that embryonic infection elicits a stronger and more coordinated antiviral response than larval-stage infection, while enabling widespread viral dissemination across diverse cell lineages. Approximately two-thirds of infected cells were derived from the nervous system or neural crest lineages, providing a potential mechanistic basis for the neurological complications occasionally reported in hNoV-infected patients. Furthermore, we identified a developmental stage-dependent role for extracellular vesicle (EV)-associated hNoV transmission: free virions mediated more efficient infection and higher symptomatic incidence in immunologically immature embryos, whereas EV-associated virions exhibited enhanced infectivity in more immunocompetent larvae. Together, these findings establish the zebrafish embryo as a versatile and accessible in vivo platform for studying symptomatic hNoV infection, reveal host maturity-dependent viral transmission strategies, and provide new opportunities for mechanistic studies and high-throughput evaluation of antiviral and vaccine candidates. Author summaryHuman norovirus is the leading cause of stomach flu worldwide but studying it has been difficult because the lack of a simple, small-animal model that actually gets sick from the virus. While older zebrafish larvae can harbor the virus, they do not show symptoms. In this study, we successfully created a new model by injecting human norovirus into zebrafish embryos at their early cell stage. Unlike the older larvae, these embryos developed clear symptoms, including fluid buildup around the heart and kidneys, tissue cloudiness, and death within three days. Using advanced genetic and metabolic tracking, we discovered that the virus spreads widely throughout the embryos body, particularly targeting cells in the nervous system. This link might explain why human patients occasionally suffer from neurological symptoms. Additionally, our study revealed that the virus changes its transmission strategy based on the animals age: it travels freely to infect vulnerable embryos but hides inside lipid vesicles to infect older, more immune-developed larvae. Ultimately, these findings provide a practical, efficient animal model to better understand norovirus sickness and rapidly test new vaccines and treatments.

microbiology↗

bioRxiv2026

(2R,6R)-Hydroxynorketamine elicits rapid antidepressant effects by promoting astrocytic μ-δ opioid receptor heterodimerization

Ketamine produces rapid antidepressant effects but is constrained by psychotomimetic properties and abuse potential. The ketamine metabolite (2R,6R)-hydroxynorketamine (HNK) shows antidepressant-like efficacy without N-methyl-D-aspartate receptor (NMDAR) blockade, yet its upstream targets remain unclear. Here we show that HNK potentiates hippocampal excitatory transmission and reverses stress-induced behavioural deficits through opioid receptor signaling. Pharmacological and genetic analyses reveal a requirement for both {micro}- and {delta}-opioid receptors in astrocytes. Chronic stress reduces {micro}-{delta} receptor heterodimers in the hippocampus, and a single dose of HNK restores their abundance. PAINT-MINFLUX nanoscopy quantifies increased {micro}-{delta} heterodimerization, and molecular dynamics simulations indicate selective binding of HNK to the {micro}-receptor protomer via Asp147 and Tyr148. Mutating these residues abolishes HNK-driven heterodimer formation, downstream signaling and rapid antidepressant-like effects in vivo. Astrocytic {micro}-{delta} opioid receptor heterodimers thus represent a targetable mechanism for next-generation rapid-acting antidepressants.

neuroscience↗

bioRxiv2026

Causally validated phase-amplitude coupling enables high-fidelity motor decoding for next-generation brain-computer interfaces

Modern Brain-Computer Interfaces (BCIs) face a fundamental performance plateau due to their reliance on broad spectral power reduction (Event-Related Desynchronization, ERD) as the primary decoding feature. ERD acts as a coarse metabolic proxy for cortical activation, discarding the high-frequency temporal syntax necessary for high-dimensional motor control. Here, we demonstrate that Phase-Amplitude Coupling (PAC)--specifically, the phase-locking of high-gamma (70-150 Hz) firing to residual Beta oscillations--provides a high-fidelity temporal feature for decoding motor intent. Using high-density electrocorticography (HD-ECoG) during motor imagery, we show that incorporating Beta-PAC into machine-learning classifiers (LDA/SVM) significantly outperforms traditional power-based features. To definitively validate the causal robustness of this feature against mathematically-derived artifacts, we leveraged a rare in vivo human structural lesion model. In a patient with focal tumor infiltration of the motor tract, the metabolic gate (ERD) was preserved, yet structural uncoupling completely abolished Beta-PAC, collapsing network topology and reducing single-trial decoding accuracy to chance levels. Our findings causally validate Beta-PAC as a robust, independent control signal, establishing a physiological foundation for next-generation, phase-dependent neuroprostheses.

neuroscience↗

bioRxiv2025

A comprehensive evaluation of ultraviolet irradiation at 254 nm and 222 nm in inactivating human noroviruses on surfaces

Human norovirus (hNoV) presents significant public health challenges due to its low infectious dose and environmental persistence. This study compared the inactivation efficacy of ultraviolet C irradiation at 254 nm (UV 254) and far-UVC radiation at 222 nm (UV 222) against four hNoV strains and two surrogate viruses, Tulane virus (TV) and bacteriophage MS2. A symptom scoring assay was developed to assess hNoV infectivity following microinjection into zebrafish embryos, being used in combination with reverse transcriptase quantitative PCR (RT-qPCR), long-range RT-qPCR, and RNase-treated RT-qPCR. With a general laboratory set-up of viruses being suspended in deionized water droplets in Petri dish, UV 222 was demonstrated with comparable, if not superior, performance in reducing hNoV infectivity and RNA integrity, and was significantly more effective than UV 254 in damaging viral capsids. MS2 exhibited inactivation patterns similar to hNoVs, whereas TV was markedly more resistant to UV 222. The performance of UV 222 was consistent in inactivating hydrated viruses on both stainless steel and porcine skin surfaces. However, the efficacy of UV-222 was substantially more reduced when virus inocula were dried or mixed with simulated vomitus containing high levels of organic matter, compared with UV-254. No evidence of viral adaptation or persistent genomic diversification was detected following repeated sublethal UV exposures. Taken together, UV 222 can be regarded as a promising technology in surface disinfection, especially for hNoV control, meantime keeping safe for human exposure. ImportanceHuman norovirus, the main cause of foodborne illness and non-bacterial gastroenteritis, can be transmitted through human-to-human contact. Indirectly, food or food related surfaces are readily contaminated by hNoV, completing the transmission route. So far, no standard cultivation tool is available for detecting viable hNoV, resulting in the challenges of evaluating inactivation effectiveness of various disinfection technologies, including UV 222 treatments. The significance of our study lays in attempts to quantify hNoV infectivity loss of four strains using zebrafish model during UV 222 and 254 treatments, together with the underlying antiviral mechanisms indicated by three different types of reverse transcription qPCR methods. In addition, the concerns over possible emergence of variant were subdued by genome wide sequencing results after consecutive UV exposures and passaging in vivo zebrafish model. SynopsisUV 222 is recommended to be applied after surface cleaning and ideally on moist surfaces.

microbiology↗

bioRxiv2025

AI recognizes convergent somatic hypermutation signatures to allow the discovery of variant-resilient broadly neutralizing antibodies

Elucidating the mechanisms by which broadly neutralizing antibodies (bnAbs) develop to confer durable immunity in humans is pivotal for the rational design of next-generation vaccines and therapeutics. VH3-53/3-66-encoded public antibodies are widely elicited in the population after the COVID-19 pandemic. Here, we isolated 15 VH3-53/3-66-encoded bnAbs from elite neutralizers who experienced sequential SARS-CoV-2 Omicron breakthrough infections. These bnAbs exhibit exceptional potency and breadth against circulating variants and, as members of a long-lived public antibody lineage, likely contribute to durable humoral protection. Genetic analysis of VH3-53/3-66-encoded bnAbs reveals a convergent somatic hypermutation pattern at seven positions in and around the CDR loops that emerges with repeated viral exposures and distinguishes them from non-bnAbs. Grafting these combined mutations onto clinically escaped antibodies broadens their breadth and restores neutralization activity. Structural analysis shows that these convergent mutations cooperatively remodel CDRs to bind and tolerate virus receptor-binding domain mutations. Using an AI-based antibody language model trained on data linking somatic hypermutations to binding affinity and neutralization, the model is able to identify mutational patterns predictive of breadth, enabling the discovery of a rare bnAb with protective activity against the latest variants from early-pandemic antibody repertoires. This demonstrates the feasibility of establishing an AI-empowered pipeline to identify mutation-tolerant bnAbs from early-pandemic antibody repertoires to fight fast-evolving newly introduced viruses.

immunology↗

bioRxiv2025

VRC01 Selects Rare HIV Escape Mutations After Acquisition in Antibody-Mediated Prevention Trials

Broadly neutralizing antibodies (bnAbs) show promise in HIV prevention, yet viral escape remains a challenge. In the Antibody Mediated Prevention (AMP) trials, the CD4 binding site (CD4bs) bNAb VRC01 blocked acquisition by VRC01-sensitive strains. However, its influence on viral evolution post-acquisition is not fully understood. Here we analyzed >12,000 HIV env sequences from 47 participants from the AMP trials, identifying VRC01-mediated de novo escape mutations in 8 of 26 VRC01-treated participants but none in 21 placebo participants. These mutations were found at very low frequency (<1%) in global viruses. Escape mutations, primarily located in the Loop-D and {beta}23/V5 regions of Env, conferred cross-resistance to several CD4bs bnAbs, while more potent CD4bs bnAbs like N6 and 1-18 largely retained their activity. Our findings demonstrate that prophylactic VRC01 can select for viral escape after infection, underscoring the need for next-generation bnAbs with improved breadth and potency to enhance durability and efficacy of antibody-based HIV prevention.

microbiology↗

bioRxiv2025

Modulating inter-mitochondrial contacts to increase membrane potential for mitigating blue light damage

Mitochondrial membrane potential (MMP) is essential for mitochondrial functions, yet current methods for modulating MMP lack precise spatial and temporal control. Here, we present an optogenetic system that enables reversible formation of inter-mitochondrial contacts (mito-contacts) with high spatiotemporal precision. Blue light stimulation induces rapid formation of mito-contacts, which fully dissipate upon cessation of illumination. These light-induced mito-contacts can enhance MMP, leading to increased ATP production under stress conditions. Moreover, in human retinal cells and C. elegans, high MMP induced by mito-contacts alleviates the deleterious effects of prolonged blue light exposure, restoring energy metabolism and extending organismal lifespan. This optogenetic approach provides a powerful tool for modulating MMP and offers potential therapeutic applications for diseases linked to mitochondrial dysfunction.

biophysics↗

bioRxiv2025

Mapping the evolution of computationally designed protein binders

Computational protein design enables the generation of binders that target specific epitopes on proteins. However, current approaches often require substantial screening from which hits require further affinity maturation. Methods for experimentally improving designed proteins and exploring their sequence-affinity landscapes could therefore streamline the development of high-affinity binders and inform future design strategies. Here, we use OrthoRep, a system for continuous hypermutation in vivo, to drive the evolution of computationally designed mini protein binders ("minibinders") that target a mammalian receptor. Despite their small sizes (59-72 amino acids), we successfully affinity matured multiple minibinders through strong selection for improved binding and also sampled new regions of minibinder fitness landscapes through extensive neutral drift. One evolved minibinder variant was used to construct a combinatorially complete sequence-affinity map for its six affinity increasing mutations, which revealed nearly full additivity in their contributions to binding. Another minibinder was subjected to both deep mutational scanning and extensive evolution under weak selection, resulting in an evolutionarily diverged collection of binder sequences that revealed non-additive relationships among mutations. Our results highlight that the affinity of computationally designed binders can be rapidly increased through evolution and provide a scalable approach for the evolutionary exploration and subsequent mapping of sequence-affinity landscapes. We suggest that this work will complement protein binder design both as a reliable experimental optimization process and as a vehicle for generating new training data.

synthetic biology↗

bioRxiv2025

Fast Multi-objective RNA Optimization with Autoregressive Reinforcement Learning

Codon optimization is essential in mRNA vaccine development, while existing tools face limitations in the computational efficiency, sequence diversity and universality. To address these challenges, we develop RNAJog (RNA Joint Optimization with autoregressive Generative model), a framework integrating autoregressive generation with reinforcement learning to optimize codon sequences for minimum free energy (MFE), codon adaptation index (CAI) and GC content, even enabling sequence design without requiring annotated training data. Evaluations in both in silico and wet-lab experiments have confirmed RNAJogs effectiveness and efficiency, with two orders of magnitude faster than traditional algorithm (LinearDesign) for long RNA sequence and about a 10-fold increase in antibody titer compared to the wild-type mRNA for Influenza virus hemagglutinin (HA) mRNA vaccine design in mouse. RNAJog also supports biological constraints for sequence optimization. Using this feature, we minimized m6A modification motifs in Bmp2 coding sequence for enhancing the translational efficiency and RNA stability, which are validated in cell-based experiments.

bioinformatics↗

bioRxiv2025

Matrix metalloproteinase-3 promotes arteriovenous fistula failure by regulating FAK-AKT signaling

Objective- Surgically created upper extremity arteriovenous fistulae (AVF) are the preferred vascular access for patients requiring dialysis. It is estimated, however, that 50% of AVF fail within one year due to aggressive neointimal hyperplasia, which significantly increases morbidity and mortality. Matrix metalloproteinase-3 (MMP-3), also known as stromelysin-1, is a member of the metalloproteinase family that plays a critical role in the pathogenesis of many human disorders by degrading extracellular matrix and regulating molecular signaling pathways. The role of MMP- 3 in AVF neointimal failure has not been explored. Approach and Results- We observed that MMP-3 was induced in a time-dependent fashion by fetal bovine serum (FBS) and the growth factor PDGF-BB in cultured venous SMC. MMP-3 was also highly expressed in the neointimal SMCs of the outflow veins and the juxta-anastomotic area in an AVF mouse model, as well as in human AVF specimens. Knockdown of MMP-3 significantly suppressed venous SMC proliferation, whereas overexpression of MMP-3 facilitated cell growth in vitro. Importantly, deficiency of global and SMC-specific MMP-3 significantly reduced neointimal hyperplasia and improved patency after AVF creation. Mechanistic studies showed that MMP-3-mediated SMC proliferation and AVF neointimal hyperplasia were regulated via the FAK-AKT signaling pathway. Conclusions- These data suggest that MMP-3 is a key mediator of AVF neointimal failure. Targeting local MMP-3 activity may be a novel therapeutic strategy to prevent AVF neointimal failure and improve outcomes in patients requiring hemodialysis.

cell biology↗

bioRxiv2025

Measure Sodium Transport in Cells with NMR

Sodium ions (Na+) are fundamental to numerous physiological functions, such as maintaining electrolyte balance, enabling nerve impulse transmission, and facilitating muscle contraction. Dysregulation of Na+ transport across cell membranes is implicated in a range of health issues, including metabolic syndromes, neurological conditions, and cardiovascular diseases. However, current methods for assessing cellular Na+ activity often face limitations; they can be invasive or fail to capture dynamic changes. In this study, we introduce a non-invasive 23Na nuclear magnetic resonance (NMR) methodology designed to directly quantify the transport rate of sodium ions in living cells. Our technique integrates relaxation exchange spectroscopy (REXSY) with a multi-site exchange model, enabling the investigation of Na+ transport dynamics on a timescale of sub-seconds. A key advantage is its ability to differentiate between intracellular and extracellular Na+ pools based on the endogenous NMR relaxation difference, thereby avoiding the need for potentially disruptive exogenous reagents. Experiments conducted on human cell lines successfully demonstrated the techniques capacity to distinguish between various physiological states, such as when ion channels are pharmacologically blocked or activated. The resulting measurements of Na+ transport rates and intracellular Na+ fractions show a clear correlation with cellular metabolic activity, offering valuable quantitative markers for monitoring transmembrane ion dynamics in vitro.

cell biology↗

bioRxiv2025

Influence of the broadly neutralizing antibody VRC01 on HIV breakthrough virus populations in antibody-mediated prevention trials

In the HIV antibody mediated prevention (AMP) trials, the broadly neutralizing antibody VRC01 demonstrated protective efficacy against new diagnoses with susceptible HIV strains. To understand how VRC01 shaped breakthrough infections, we performed deep sequencing on 172 participants in the placebo and treatment arms, generating 63,444 gag-{Delta}pol (2.5 kb) and 53,088 rev-env-{Delta}nef (3 kb) sequences. Sequences were classified into transmitted founder lineages (TFLs), and infections with multiple distinct lineages were determined. Multilineage infections were detected in [~]38% of participants in both the African (HVTN 703/HPTN 081) and Americas/Europe (HVTN 704/HPTN 085) cohorts, regardless of placebo or treatment group, or cohort. The high levels of multilineage infections could be attributed to minor lineages (<5% abundance) identified in 20% of participants. Infection with VRC01 discordant viruses (IC80s >3-fold different) was observed in 40% of multilineage infections, with a trend toward greater intra-host neutralization differences with increasing VRC01 dose (Jonckheere-Terpstra test, p=0.072). In six VRC01 treated participants who acquired both sensitive (IC80<1{micro}g/ml) and resistant viruses (IC80>3{micro}g/ml), the sensitive lineages declined over time. Recombination was pervasive, observed in 63% of multilineage infections at the time of HIV diagnosis. In one treated participant infected with VRC01 discordant lineages, recombinant viruses preferentially inherited the resistance mutation (binomial p=0.004). In conclusion, our in-depth analysis of breakthrough viruses in the AMP trials revealed a high frequency of multilineage infections, including infections with viruses with different VRC01 sensitivities. This analysis also highlights the role of recombination in shaping intra-host viral evolution and facilitating escape from VRC01. SignificanceThis work advances our understanding of the diversity of initial viral infection and evolution and in vivo activity of broadly neutralizing antibodies (bNAbs). Deep sequencing revealed [~]38% of HIV acquisitions with multiple transmitted founder lineages, higher than previous studies. These occurrences were similar in the placebo and VRC01 groups. Viral recombination among post-acquisition variants was common under antibody selection and appeared to favor resistant sequences in the treatment group. These data suggest as with single antiviral therapy, passive and active immunization of bNAbs should be directed at multiple antigen targets of HIV-1.

molecular biology↗

bioRxiv2025

Peroxisomal import is circadian in glia and regulates sleep and lipid metabolism

Peroxisomes are critical organelles that detoxify cellular waste while also catabolizing and anabolizing lipids. How peroxisomes coordinate protein import and support metabolic functions across complex tissues and timescales remains poorly understood in vivo. Using the Drosophila brain, we discover a striking enrichment of peroxisomes in the neuronal soma and the cortex glia that enwrap them. Unexpectedly, import of peroxisomal proteins into cortex glia, but not neurons, oscillated across time and peaked in the early morning. Rhythmic peroxisomal import in cortex glia autonomously required the circadian clock and Peroxin 5 (Pex5; peroxisomal biogenesis factor 5 homolog), with import persistently elevated in clock mutants. Notably, reducing Pex5 in cortex glia, but not neurons, caused hyperactivity and reduced total sleep. Moreover, brain lipid metabolism was dramatically altered upon Pex5 knockdown, with glia impacting sphingolipids and triacylglycerols, and neurons impacting phospholipids. The cell-type specificity of these Pex5 phenotypes highlights unique roles for peroxisomal import in both sleep and lipid metabolism in the brain.

neuroscience↗

bioRxiv2025

The XPF-like domain in SHOC1 required for homologous recombination and safeguarding autosome from meiotic silencing of unsynapsed chromatin

During meiosis, a group of evolutionarily conserved ZMM proteins plays essential roles in stabilizing the recombination intermediates and promoting crossover (CO) formation. In mice, SHOC1 forms a trimeric complex with the other two ZMM proteins, SPO16 and TEX11, to bind recombination intermediates after strand invasion. Although genetic variants of SHOC1 are clinically associated with meiotic arrest and male infertility, their precise molecular mechanisms and evolutionarily conserved functions in human gametogenesis remain enigmatic. Here, we delineated species-specific divergences between human and mouse SHOC1 complex, and identified a missense variant within the XPF-like domain in SHOC1 (c.A1769G:p.Q590R) that was associated with meiotic arrest and non-obstructive azoospermia (NOA). The disorder of the XPF-like domain in SHOC1 impaired DNA double-strand breaks repair by compromising its ability to bind branched DNA structures and the recruitment of M1AP, REDIC1, and ZMM factors to recombination intermediates, ultimately abolishing CO formation. Furthermore, the variant disrupted dynamic 3D chromatin structure in pachytene spermatocytes and induced defects in homologous chromosome synapsis. More importantly, the XPF-like domain in SHOC1 was revealed to prevent autosome intrusion into the sex body compartment, thereby safeguarding critical autosomal loci from meiotic silencing of unsynapsed chromatin (MSUC). Overall, our study demonstrated that the XPF-like domain in SHOC1 is required for homologous recombination and safeguarding autosome from MSUC in meiosis.

developmental biology↗